From: Justine Raymond (jraymond_at_ICIQ.ES)
Date: Wed Jun 10 2020 - 09:23:34 CDT
Hello everyone
I am very new to using namd2 to perform MD simulation.
I am trying to perform a protein ligand complex. I am doing a first minimization only of the water and ions first so there on the protein and the ligand and then, I want to minimize the whole system altogether in 2000 steps. The simulation seems to run fine but when I try to then equilibrate the system I get the followin error from the beginning. I have looked already in previous posts about it, I have tried extending the size of the cell increasing the temperature gradually but it does not seem to help. If I change the time step from 2 to 1 fs it is working but I am afraid that I might just be avoiding a bigger problem
I do not know if it is problem of parametrization of my system of my configuration file or what I am missing. I am have obtained the parameter file of the ligand from CHARMM-GUI. Is there a way for me to make sure that my system is viable ? I could run the same simulation with the apo protein without any problem, so I am not sure if the problem come from the presence of the ligand and may be I should right the conf file differently, or if the parameters are not okay.
I would really appreciate some help. I have uploaded on a drive the conf file of the minimization (minimization with protein ligand complex restrained), minimization 1 (second minimization with the whole system), equilibration and I have also uploaded the log file obtained. I would be so grateful if someone could help spot how I could solve this issue.
THank you SO MUCH
Justine R.
Universitat Rovira i Virgili
https://drive.google.com/drive/folders/1cl46T8bCRXBjDS3XaN2fy7HQFgJNBVhb?usp=sharing
THE ERROR:
TCL: Running for 100000 steps
PRESSURE: 0 -2598.35 -42.5154 34.7801 -42.6547 -2693.69 48.8195 34.8098 48.4652 -2616.21
GPRESSURE: 0 -2551.07 -40.8064 35.906 -41.4789 -2650.7 52.3577 35.019 52.0307 -2565.87
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 606.2925 1910.5606 5017.0367 65.5167 -769994.1439 88258.8534 0.0047 0.0000 0.0000 -674135.8793 0.0000 -674135.8793 -674134.8956 0.0000 -2636.0820 -2589.2111 1898775.0000 -2636.0820 -2589.2111
OPENING EXTENDED SYSTEM TRAJECTORY FILE
ERROR: Atom 9427 velocity is 1710.06 -2074.37 -5416.05 (limit is 6000, atom 373 of 584 on patch 74 pe 44)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 74 pe 44).
FATAL ERROR: Exiting prematurely; see error messages above.
[Partition 0][Node 0] End of program
THE CONF FILE:
cutoff 12.0
pairlistdist 14.0
switching on
switchdist 10.0
PME on
PMEGridspacing 1
wrapAll on
wrapWater on
##START HERE###
##Simulation Template##
# Simulation conditions
coordinates system.pdb
structure system.psf
binCoordinates Minimization.1.restart.coor
binVelocities Minimization.1.restart.vel
extendedSystem Minimization.1.restart.xsc
# Simulation conditions
#temperature 60
# Harmonic constraints
constraints on
consref Minimization.1.coor
conskfile constraint.pdb
constraintScaling 2
consexp 2
conskcol B
# Output Parameters
binaryoutput no
outputname Equilibration
outputenergies 1000
outputtiming 1000
outputpressure 1000
binaryrestart yes
dcdfile Equilibration.dcd
dcdfreq 2000
XSTFreq 2000
restartfreq 2000
restartname Equilibration.restart
# Thermostat Parameters
langevin on
langevintemp 310
langevinHydrogen off
langevindamping 1
# Barostat Parameters
langevinpiston on
usegrouppressure yes
useflexiblecell no
useConstantArea no
langevinpistontarget 1.01325
langevinpistonperiod 200
langevinpistondecay 100
langevinpistontemp 310
# Integrator Parameters
timestep 2
firstTimestep 0
fullElectFrequency 2
nonbondedfreq 1
# Force Field Parameters
paratypecharmm on
parameters toppar_water_ions_namd.str
parameters toppar_all36_carb_glycopeptide.str
parameters par_all36_lipid.prm
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_all36_carb.prm
parameters par_all36_cgenff.prm
parameters lig1.prm
exclude scaled1-4
1-4scaling 1.0
rigidbonds all
#Implicit Solvent Parameters
gbis off
alphaCutoff 14.0
ionConcentration 0.15
run 100000
set file [open Equilibration.check w+]
set done 1
if {[file exists Equilibration.restart.coor] != 1 || [file exists Equilibration.restart.vel] != 1 || [file exists Equilibration.restart.xsc] != 1 } {
set done 0
}
if {$done == 1} {
puts $file "DONE"
flush $file
close $file
} else {
puts $file "One or more files failed to be written"
flush $file
close $file
}
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